:: DESCRIPTION
Assemblet is a short read assembler for assembling antigenic variant sequences in bacteria.
::DEVELOPER
Victorian Bioinformatics Consortium
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.
::DEVELOPER
INRA, URGI
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tedna: a Transposable Element De Novo Assembler.
Zytnicki M, Akhunov E, Quesneville H.
Bioinformatics. 2014 Jun 3. pii: btu365.
:: DESCRIPTION
ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. 2002.
ARACHNE: a whole-genome shotgun assembler.
Genome Research12: 177–189.
Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. 2003.
Whole-genome sequence assembly for mammalian genomes: Arachne 2.
Genome Research 13: 91–96.
Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB. 2009.
Assisted assembly: how to improve a de novo genome assembly by using related species.
Genome Biology10: R88.
:: DESCRIPTION
SSP is a de novo transcriptome assembler that assembles RNA-seq reads into transcripts. SSP aims to reconstructs all the alternatively spliced isoforms and estimates the expression level of them.
::DEVELOPER
School of Biological Sciences, Iran
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ViSpA (Viral Spectrum Assembling) implements a novel viral assembling and frequency estimation methods. This software uses a simple error correction, viral variants assembling based on maximum-bandwidth paths in weighted read graphs and frequency estimation via Expectation Maximization on all reads.
::DEVELOPER
Georgia State University NGS Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2011;12 Suppl 6:S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.
Inferring viral quasispecies spectra from 454 pyrosequencing reads.
Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A.
:: DESCRIPTION
EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Weichun Huang and Gabor Marth
EagleView: a genome assembly viewer for next-generation sequencing technologies,
Genome Res.,June 11, 2008
:: DESCRIPTION
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads, while also achieves both transcripts parsimony and coverage deviation minimization.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Biotechnol. 2017 Dec;35(12):1167-1169. doi: 10.1038/nbt.4020.
Accurate assembly of transcripts through phase-preserving graph decomposition.
Shao M, Kingsford C.
:: DESCRIPTION
KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler, which enables to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 300M reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix,
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
BMC Bioinformatics 2012, 13(Suppl 6):S5
:: DESCRIPTION
PEAR is an ultrafast, memory-efficient and highly accurate pair-end reads assembler. It is fully parallelized and can run with as low as just a few kilobytes of memory.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Mar 1;30(5):614-20. doi: 10.1093/bioinformatics/btt5
PEAR: A fast and accurate Illumina Paired-End reAd mergeR.
Zhang J, Kobert K, Flouri T, Stamatakis A.
:: DESCRIPTION
IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.
::DEVELOPER
Pathogen Informatics, Wellcome Trust Sanger Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.
Bioinformatics. 2015 Feb 28. pii: btv120.
